Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs.
Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs.
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DOI：
10.3389/fnut.2021.742672
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发表时间：
2021
影响因子：
5
通讯作者：
Zhou L
中科院分区：
文献类型：
--
作者：
Miao W;Ma Z;Tang Z;Yu L;Liu S;Huang T;Wang P;Wu T;Song Z;Zhang H;Li Y;Zhou L
陆川猪是我国典型的肥胖猪种，其背最长肌肌纤维的直径和面积明显小于杜洛克（瘦肉型）猪。骨骼肌纤维特性与家畜的肉质有关。不同品种猪肉的品质与肌纤维特性之间存在显著的相关性，肌纤维特性是影响猪肉品质的重要因素。肌纤维的直径和面积与肌肉的生长发育有关。因此，我们使用转座酶可接近染色质测序（ATAC-seq）和RNA测序（RNA-seq）分析来研究两种类型猪之间骨骼肌生长和发育差异的潜在机制。首先，分析转座酶可接近的染色质以绘制开放染色质区域和转录因子结合位点的景观。我们鉴定了几种可能影响肌肉生长和发育的转录因子，包括TFAP 4、MAX、NHLH 1、FRX 5和TGIF 1。我们还发现，具有基本螺旋-环-螺旋结构的转录因子优先与肌肉发育相关基因结合。然后，通过整合ATAC-seq和RNA-seq，我们发现Wnt信号通路，mTOR信号通路和其他经典通路调节骨骼肌发育。此外，一些可能调节骨骼肌生长的途径，如甲状旁腺激素的合成、分泌和作用，酮体的合成和降解，以及甲状腺激素信号通路，这些都被显著富集。经过进一步的研究，我们确定了一些可能与肌肉发育相关的候选基因（ASNS，CARNS 1，G 0 S2，PPP 1 R14 C和SH 3BP 5）。我们还发现，在某些基因水平上的染色质开放的差异调节与在转录水平上的差异调节相反，这表明转录因子和转录抑制因子可能参与了基因表达的调节。本研究为深入了解两种猪肌纤维差异的机理提供了依据，为进一步研究改善猪肉品质提供了重要基础。
Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.
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